X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FDiscoverer.java;h=ba4054e27164a9bea8166ec8d8350ef9fb3f373b;hb=e957648a02a9e25795a92a4f39a5e3c1e7adb230;hp=d544bea9de4da5c4f65147273767f63b467b891e;hpb=e5b2fbdb4ecc9faaadcc3e18fabad8794fca44aa;p=jalview.git

diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java
index d544bea..ba4054e 100644
--- a/src/jalview/ws/jws1/Discoverer.java
+++ b/src/jalview/ws/jws1/Discoverer.java
@@ -20,14 +20,13 @@
  */
 package jalview.ws.jws1;
 
+import jalview.gui.JvOptionPane;
 import jalview.util.MessageManager;
 
 import java.util.Hashtable;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
-import javax.swing.JOptionPane;
-
 import ext.vamsas.IRegistry;
 import ext.vamsas.IRegistryServiceLocator;
 import ext.vamsas.RegistryServiceSoapBindingStub;
@@ -193,35 +192,37 @@ public class Discoverer implements Runnable
         jalview.bin.Cache.log.debug("Setting default services");
         services = new Hashtable();
         // Muscle, Clustal and JPred.
-        ServiceHandle[] defServices =
-        {
+        ServiceHandle[] defServices = {
             new ServiceHandle(
                     "MsaWS",
                     "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment "
                             + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
                     "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
-                    MessageManager.getString("label.muscle_multiple_protein_sequence_alignment")),
+                    MessageManager
+                            .getString("label.muscle_multiple_protein_sequence_alignment")),
             new ServiceHandle(
                     "MsaWS",
                     "Katoh, K., K. Kuma, K., Toh, H.,  and Miyata, T. (2005) "
                             + "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\""
                             + " Nucleic Acids Research, 33 511-518",
                     "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS",
-                    MessageManager.getString("label.mafft_multiple_sequence_alignment")),
+                    MessageManager
+                            .getString("label.mafft_multiple_sequence_alignment")),
             new ServiceHandle(
                     "MsaWS",
                     "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"
                             + " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
                             + " Nucleic Acids Research, 22 4673-4680",
                     "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
-                    MessageManager.getString("label.clustalw_multiple_sequence_alignment")),
+                    MessageManager
+                            .getString("label.clustalw_multiple_sequence_alignment")),
             new ServiceHandle(
                     "SecStrPred",
                     "Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)\nJPred4: a protein secondary structure prediction server"
                             + "\nNucleic Acids Research, Web Server issue (first published 15th April 2015)"
                             + "\ndoi://10.1093/nar/gkv332",
                     "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred",
-                    "JNet Secondary Structure Prediction") };
+                    "JPred Secondary Structure Prediction") };
         services = new Hashtable();
         serviceList = new Vector();
         buildServiceLists(defServices, serviceList, services);
@@ -253,12 +254,11 @@ public class Discoverer implements Runnable
       {
         if (jalview.gui.Desktop.desktop != null)
         {
-          JOptionPane
-                  .showMessageDialog(
-                          jalview.gui.Desktop.desktop,
-                          MessageManager.getString("label.set_proxy_settings"),
-                          MessageManager.getString("label.proxy_authorization_failed"),
-                          JOptionPane.WARNING_MESSAGE);
+          JvOptionPane.showMessageDialog(jalview.gui.Desktop.desktop,
+                  MessageManager.getString("label.set_proxy_settings"),
+                  MessageManager
+                          .getString("label.proxy_authorization_failed"),
+                  JvOptionPane.WARNING_MESSAGE);
         }
       }
       else
@@ -382,11 +382,13 @@ public class Discoverer implements Runnable
   /**
    * creates a new thread to call discoverServices()
    */
+  @Override
   public void run()
   {
     final Discoverer discoverer = this;
     Thread discoverThread = new Thread()
     {
+      @Override
       public void run()
       {
         discoverer.doDiscovery();